I am currently using OroCRM as a base CRM for financial advisors. As such, I have no need for the MagentoBundle because the advisors have no need to track online orders, carts, etc. Is just deleting the MagentoBundle the best way to remove the it? I have tried this, however I still see some residual MagentoBundle stuff laying around (i.e. System > Entities) in the admin. Is there a clean way to remove or disable CRM bundles? Or is there a way to not even install the MagentoBundle as part of the installation process in the first place?

You can disable any bundle in AppKernel.php (that’s way how symfony works).Here is an example for you.

So in case when you are able to reinstall CRM this will solve your issue(need to drop and create database from scratch). But if you already have a lot of data, this will just disable a bundle and you should to clean up database manually(Doctrine ORM don’t have way to clean up DB). Also our WorkflowBundle and EntityConfigBundle are not able to cleanup data automatically.